[2024-01-24 11:44:38,168] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg0081ce59-41d0-4e44-a0d6-3f0b35441487/dqc_reference
[2024-01-24 11:44:41,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,488] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg824e3328-524e-4a45-9a6b-41c53f9a0cdb/GCF_014926585.1_ASM1492658v1_genomic.fna.gz | prodigal -d GCF_014926585.1_ASM1492658v1_genomic.fna/cds.fna -a GCF_014926585.1_ASM1492658v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:54,727] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:54,728] [INFO] Task started: HMMsearch
[2024-01-24 11:44:54,728] [INFO] Running command: hmmsearch --tblout GCF_014926585.1_ASM1492658v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0081ce59-41d0-4e44-a0d6-3f0b35441487/dqc_reference/reference_markers.hmm GCF_014926585.1_ASM1492658v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:54,998] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:54,999] [INFO] Found 6/6 markers.
[2024-01-24 11:44:55,038] [INFO] Query marker FASTA was written to GCF_014926585.1_ASM1492658v1_genomic.fna/markers.fasta
[2024-01-24 11:44:55,038] [INFO] Task started: Blastn
[2024-01-24 11:44:55,039] [INFO] Running command: blastn -query GCF_014926585.1_ASM1492658v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0081ce59-41d0-4e44-a0d6-3f0b35441487/dqc_reference/reference_markers.fasta -out GCF_014926585.1_ASM1492658v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:55,948] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:55,952] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:55,952] [INFO] Target genome list was writen to GCF_014926585.1_ASM1492658v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:56,006] [INFO] Task started: fastANI
[2024-01-24 11:44:56,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg824e3328-524e-4a45-9a6b-41c53f9a0cdb/GCF_014926585.1_ASM1492658v1_genomic.fna.gz --refList GCF_014926585.1_ASM1492658v1_genomic.fna/target_genomes.txt --output GCF_014926585.1_ASM1492658v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:07,295] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:07,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0081ce59-41d0-4e44-a0d6-3f0b35441487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:07,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0081ce59-41d0-4e44-a0d6-3f0b35441487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:07,307] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:07,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:07,307] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	100.0	1349	1349	95	conclusive
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	82.6431	828	1349	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	81.7176	782	1349	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	81.5524	805	1349	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	81.5056	735	1349	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	81.4907	799	1349	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	81.4656	757	1349	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	80.9003	718	1349	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	80.8529	753	1349	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.7896	704	1349	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	80.7312	666	1349	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.8288	609	1349	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	77.4502	322	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:07,309] [INFO] DFAST Taxonomy check result was written to GCF_014926585.1_ASM1492658v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:07,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:07,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:07,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0081ce59-41d0-4e44-a0d6-3f0b35441487/dqc_reference/checkm_data
[2024-01-24 11:45:07,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:07,356] [INFO] Task started: CheckM
[2024-01-24 11:45:07,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014926585.1_ASM1492658v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014926585.1_ASM1492658v1_genomic.fna/checkm_input GCF_014926585.1_ASM1492658v1_genomic.fna/checkm_result
[2024-01-24 11:45:47,854] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:47,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:47,875] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:47,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:47,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014926585.1_ASM1492658v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:47,876] [INFO] Task started: Blastn
[2024-01-24 11:45:47,876] [INFO] Running command: blastn -query GCF_014926585.1_ASM1492658v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0081ce59-41d0-4e44-a0d6-3f0b35441487/dqc_reference/reference_markers_gtdb.fasta -out GCF_014926585.1_ASM1492658v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:49,603] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:49,606] [INFO] Selected 11 target genomes.
[2024-01-24 11:45:49,607] [INFO] Target genome list was writen to GCF_014926585.1_ASM1492658v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:49,616] [INFO] Task started: fastANI
[2024-01-24 11:45:49,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg824e3328-524e-4a45-9a6b-41c53f9a0cdb/GCF_014926585.1_ASM1492658v1_genomic.fna.gz --refList GCF_014926585.1_ASM1492658v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014926585.1_ASM1492658v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:00,019] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:00,059] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:00,059] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014926585.1	s__Devosia sp014926585	100.0	1349	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005222805.1	s__Devosia sp005222805	83.8669	890	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	83.2785	885	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_018334155.1	s__Devosia sp018334155	83.0447	862	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110945.1	s__Devosia sp900110945	82.7086	810	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427605.1	s__Devosia sp001427605	82.665	820	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859655.1	s__Devosia ginsengisoli	82.6305	829	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860165.1	s__Devosia sp014860165	82.6076	839	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820005.1	s__Devosia sp018820005	82.0694	503	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698645.1	s__Devosia sp016698645	81.708	783	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128975.1	s__Devosia limi	81.4854	756	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:00,061] [INFO] GTDB search result was written to GCF_014926585.1_ASM1492658v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:00,065] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:00,069] [INFO] DFAST_QC result json was written to GCF_014926585.1_ASM1492658v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:00,069] [INFO] DFAST_QC completed!
[2024-01-24 11:46:00,069] [INFO] Total running time: 0h1m22s